nirs4all-papers

Public archive for deposited nirs4all papers and reproducible public code bundles.

Part of the open-source NIRS tools ecosystem: file readers, datasets, methods, browser modelling, reproducible pipelines, papers, benchmarks, and release dashboards for near-infrared spectroscopy.

This repository is for material that can be public and permanent:

• accepted/deposited paper PDFs;
• reproducibility kits;
• public data references and download scripts;
• frozen code used for a paper result;
• WASM/static builds linked from nirs4all.org;
• DOI, tag, release, and provenance metadata.

Drafts, reviewer-private material, journal scouting, private datasets, and in-progress manuscripts belong in the private nirs4all-drafts repository.

Lifecycle

1. Work happens privately in nirs4all-drafts and experimentally in nirs4all-lab.
2. Once the draft and lab work are ready for public release, move only the deposited PDF and reproducible public code here.
3. Build a stable WASM/static artifact when the paper needs an interactive public companion.
4. Link the released paper bundle from nirs4all.org.

Layout

papers/
  README.md
templates/
  reproducibility-kit/
    README.md

Each paper should use a stable slug, for example:

papers/2026-aom-transfer/
  README.md
  paper.pdf
  CITATION.cff
  code/
  data/
  wasm/

Do not commit generated caches, private review files, unpublished drafts, or data that cannot be redistributed.

Reproduction-document publisher

n4a-papers turns a deposited .n4a bundle plus a short paper.yaml into a self-contained reproduction page — the exact pipeline, a bibliography for every method, the protocol and scores, a live in-browser replay that re-runs the pipeline, and deposit sidecars (CITATION.cff, BibTeX, RO-Crate). It builds a static site for papers.nirs4all.org.

pip install nirs4all-papers     # the publisher CLI (or: pip install -e . from a checkout)
n4a-papers build --out site     # papers/*/  →  ./site  (open site/index.html)

See docs/REPRODUCTION_PUBLISHER.md for the design and papers/README.md for the per-paper bundle layout.

Provider/plugin facade

For core/UI/provider clients, nirs4all-papers also exposes a thin first-party facade in nirs4all_papers.provider. It stays archive-local and write-bounded:

• reads: list_papers, load_paper, load_paper_bundle, inspect_bundle, build_methods_section, citation, bibtex;
• explicit local output only: build_repro_page, export_sidecars.

The facade does not execute pipelines, upload artifacts, or write back into repository, datasets, or benchmark stores.

License

This repository — reproducibility code and accompanying content alike — is dual-licensed open-source — CeCILL-2.1 OR AGPL-3.0-or-later — with an optional commercial license (for any commercial use, contact nirs4all-admin@cirad.fr), matching the rest of the nirs4all ecosystem. Deposited manuscripts carry their publisher's terms, and datasets / third-party assets keep their upstream terms. See LICENSING.md and LICENSES/.